Control Region Length Dynamics Potentially Drives Amino Acid Evolution in Tarsier Mitochondrial Genomes

Patterns and processes of molecular evolution critically influence inferences in phylogeny and phylogeography. Within primates, a shift in evolutionary rates has been identified as the rationale for contrasting findings from mitochondrial and nuclear DNA studies as to the position of Tarsius. While the latter now seems settled, we sequenced complete mitochondrial genomes of three Sulawesi tarsiers (Tarsius dentatus, T. lariang, and T. wallacei) and analyzed substitution rates among tarsiers and other primates to infer driving processes of molecular evolution. We found substantial length polymorphism of the D-loop within tarsier individuals, but little variation of predominant lengths among them, regardless of species. Length variation was due to repetitive elements in the CSB domain—minisatellite motifs of 35 bp length and microsatellite motifs of 6 bp length. Amino acid evolutionary rates were second highest among major primate taxa relative to nucleotide substitution rates. We observed many radical possibly function-altering amino acid changes that were rarely driven by positive selection and thus potentially slightly deleterious or neutral. We hypothesize that the observed pattern of an increased amino acid evolutionary rate in tarsier mitochondrial genomes may be caused by hitchhiking of slightly deleterious mutations with favored D-loop length variants selected for maximizing replication success within the cell or the mitochondrion.     

Phylogenetic and genetic characterization of Acidithiobacillus strains isolated from different environments

To study the phylogenetic relationships and genetic heterogeneity of 21 Acidithiobacillus strains isolated from different environments, we amplified and sequenced the 16S–23S rRNA gene intergenic spacers (ITS) of all these strains. These sequence data, combined with related sequences available from GenBank, were divided into six phylogenetic groups by 16S rRNA gene and by 16S–23S rRNA gene sequence analysis. The results of phylogenetic analysis were consistent with those obtained by repetitive element PCR and arbitrarily primed PCR. In this research, the Acidithiobacillus ferrooxidans (A. ferrooxidans) strains were always separated into two groups in phylogenetic and cluster analyses. Genotypic analyses of the genes rusA, rusB, hip and iro suggest that these two groups may have different biochemical mechanisms for oxidizing ferrous iron. Strains in one A. ferrooxidans group were detected with rusA gene that encodes rusticyanin A which plays a very important role in the iron respiratory chain. The second A. ferrooxidans group was found to contain rusB gene which encode a homologous protein (RusB). The data suggested that ITS-based phylogeny is an effective tool to elucidate the relationships of Acidithiobacillus and that a different iron oxidation pathway may exist in different A. ferrooxidans groups.     

Taxonomic and phylogenetic significance of seed coat microsculpturing in Mentzelia (Loasaceae) in Wyoming and adjacent western states

Six hundred seeds belonging to the genusMentzelia (Loasaceae) were examined using the Scanning Electron Microscope. The seeds represented all six sections of the genus and approximately 76% of the total number of species from northern Mexico and western United States. Emphasis was placed on seed material from Wyoming and adjoining states. Ovule serial sectioning was done to determine testa ontogeny. In all cases seed surface structures could be related to excrescences developing from the integument cells. Six basic seed coat relief features could be distinguished, corresponding to the six sections in the genus. Minor variations in the basic types are constant and characteristic for species or, in very few instances, for species groups. A dendrogram was constructed from the seed testa data which supports the phylogeny established from chromosomal and morphological data. Practical application of seed coat microcharacter specificity to identification ofMentzelia seeds from prehistoric sites is suggested.     

Evolution of ancient lake bivalves: the Lymnocardiinae (Cardiidae) of the Caspian Sea

The Caspian Sea as the largest continental water body in the world is known for its comparably high levels of biodiversity and endemism, also in mollusks. The evolution of a euryhaline taxon of cardiid bivalves, the Lymnocardiinae of the Ponto-Caspian region, remains unclear today. We studied material from the whole recent range of Lymnocardiinae (i.e., the Caspian, the Azov, and the Black Seas) using a LSU rDNA phylogeny aiming at (a) testing the monophyly of Lymnocardiinae and (b) determining the phylogenetic relationships within Cardiidae. Lymnocardiinae s.str. were monophyletic, i.e., a distinct group that included species of Hypanis, Didacna, and Monodacna. Lymnocardiinae as often understood, i.e., including Cerastoderma, are not monophyletic in our analysis and Cerastoderma should thus be transferred to Cardiinae. The Lymnocardiinae s.str. had a shallow tree topology and were poorly resolved. No clearcut biogeographical pattern could be derived from the phylogeny, i.e., species stemming from respective Ponto-Caspian regions, do not necessarily cluster together. We discuss a scenario of the evolutionary history and biogeographical (as well as taxonomic) implications. Given the complex history of the Ponto-Caspian region and the Caspian Sea in particular, the Lymnocardiinae would represent an interesting study object for addressing the consequences of environmental changes on biotic evolution at various spatial and temporal scales.     

Complete mitochondrial genomes of Ceratobaeus sp. and Idris sp. (Hymenoptera: Scelionidae): shared gene rearrangements as potential phylogenetic markers at the tribal level

We sequenced the complete mitochondrial genomes of two sceliond taxa (Ceratobaeus sp. and Idris sp.). An atypical tRNA-Arg which lacks a D-stem was identified in both taxa, and represents a potentially derived character of sceliond wasps. A number of tRNA genes have rearranged in the two mitochondrial genomes compared with the ancestral organization. Some of these derived genome organizations are shared, and thus have much potential as phylogenetic markers at the tribal level in the subfamily Scelioninae. We test the influence of third codon inclusion/exclusion, alignment methods and partition schemes on the reconstruction of phylogenetic relationships. The results show that inclusion of third codon positions does not appear to be problematic when investigating the phylogeny of closely related taxa. Muscle and PartitionFinder schemes significantly improve the likelihood scores.     

Comparison of numerical taxonomic methods used to estimate flavonoid similarities in the Limnanthaceae

The Limnanthaceae is a small family of North American herbs with uncertain internal relationships. Taxa of the family were compared on the basis of 46 flavonol glycosides occurring in all plant tissues or in petals only. The flavonoid data were analyzed by 3 numerical taxonomic techniques: 1) clustering by the Weighted Pair Group method considering positive and negative matches (Using Simple Matching coefficient) ; 2) clustering by the Weighted Pair Group method considering only positive matches (using Jaccard coefficient) ; 3) Varimax Factor Analysis with rotation. No significantly different results were produced by the two clustering methods. Factor analysis provided a clearer indication of relationships among taxa of the Limnanthaceae than did conventional clustering analysis. Apparently, ordination of taxa in three dimensions is necessary to accurately express relationships between divergent evolutionary lines of the family since much of the expressed variation in flavonoids cannot be accounted for by a one-dimensional clustering technique.     

Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitation and insights into chromosome evolution

Background and Aims

Species'' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species'' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species'' identification.

Methods

Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes.

Key Results

Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species'' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands.

Conclusions

The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic data proved to be a valuable source of information to understand evolutionary patterns within Maxillariinae orchids.Key words: Chromosome number, Christensonella, Cymbidieae, cytotaxonomy, fluorochrome staining, Maxillaria, Maxillariinae, molecular phylogenetics, species delimitation     

Atlas of foliar surface features in woody plants,IX. Betulaceae of eastern United States

Scanning electron microscopy was used to examine foliar surface features such as cuticular patterns, epicuticular wax, and trichome types in species ofAlnus, Betula, Carpinus, Corylus, andOstrya. Six trichome types are recognized in this survey, four non-glandular (acicular, filiform, aduncate, subulate) and two glandular (stipitate gland and peltate scale). The distribution of these trichomes among the genera supports the recognition of two tribes, Betuleae (Alnus andBetula) and Coryleae (Carpinus, Corylus, andOstrya). Trichome morphology can be an important supportive taxonomic character in determining evolutionary relationships.     

Cytotaxonomy ofCalliphoridae (Diptera)

A modification of the general system of classification ofCalliphoridae is proposed in this report. Information about the chromosome complements of about 90 species is provided including references to the earlier literature on chromosomes of this family. With one exception all species studied by us or by earlier investigators have 2n=12. The total complement length of 556 complements from 83 species averaged 66.4 μ. Most species have a short heteromorphic sex pair but the size and morphology vary considerably and one species,Hemipyrellia fernandica, seems to have a quadrivalent sex-chromosome complex in a 2n=14 complement. The autosomal pairs vary in both length and arm ratios between the species but seem to be more stable than the sex chromosomes. Only minor variations were found between different collections of the same species except for two collections ofCalliphora croceipalpis. Although presently available data on the chromosomes of Diptera species suggest that increases in total complement length accompany evolutionary progress, no such general trends were obvious in either the total complement lengths or chromosome morphology, either within or between the tribes ofCalliphoridae. Thus the karyotypical reorganizations in the family have apparently not been directly associated with changes in the general morphological features of the adults which may have responded in these respects more extensively to genetic mutations.     

Negative Purifying Selection Drives Prion and Doppel Protein Evolution

The prion protein (PrP) when misfolded into the pathogenic conformer PrP^Sc is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary pressure on the corresponding gene using different datasets have yielded conflicting results. In addition, putative PrP or PrP interacting partners with strong similarity to PrP such as the doppel protein have not been examined to determine if the same evolutionary mechanisms apply to prion paralogs or if there are coselected sites that might indicate how and where the proteins interact. We examined several taxonomic groups that contain model organisms of prion diseases focusing on primates, bovids, and an expanded dataset of rodents for selection pressure on the prion gene (PRNP) and doppel gene (PRND) individually and for coevolving sites within. Overall, the results clearly indicate that both proteins are under strong selective constraints with relaxed selection on amino acid residues connecting α-helices 1 and 2.     

A systematic study of the genus hulsea (Asteraceae)

A systematic treatment based on genetic, biochemical, and morphological studies is presented for the 11 recognized taxa ofHulsea. A uniform diploid complement of 38 chromosomes was found in the 37 populations examined, including all species and representing first reports forH. brevifolia, H. californica, andH. mexicana. Thirteen flavonoid compounds, based on the aglycones quercetin, apigenin, cyanidin, and the 4′-O-methyl ether of luteolin, were detected inHulsea. Patterns of the flavonoid compounds are discussed with respect to the systematic treatment. The results of 595 synthetic crosses indicate thatHulsea species are self-incompatible, relatively cross-compatible, and that their F₁ hybrids are relatively fertile. Heterozygosity for one or two translocations is reported for 11 interspecific and intersubspecific hybrid combinations.     

Barnacle Goose (Branta leucopsis) feeding ecology and trophic relationships on Kolguev Island: The usage patterns of nutritional resources in tundra and seashore habitats

Insight into colonization of new areas by invasive species and their relationships with aboriginal species is a major challenge in ecology, allowing for prediction of the outcome of biological invasions. In this context, the current expansion of the Barnacle Goose (Branta leucopsis) is of great interest. The seasonal dynamics of Barnacle Goose feeding and the structure of its diet on Kolguev Island during the nesting and postnesting periods (May 27–July 29) have been examined. The diet structures of the invasive Barnacle Goose and the aboriginal species White-fronted goose (Anser albifrons) and Bean goose (A. fabalis) have been compared. The probability of interspecific competition and the ecological advantages in the diet patterns of these species have been estimated. If the Barnacle Goose population on Kolguev Island continues to increase, this may led to a decline in the population of aboriginal species of geese on the island.     

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot

Background

Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.

Methodology/Principal Findings

Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.

Conclusions/Significance

As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.     

Isolation and functional characterization of a novel gene coding for flavonoid 3′-hydroxylase from globe artichoke

Globe artichoke (Cynara cardunculus L. var. scolymus) is rich in flavonoids which contribute to its health-promoting properties. With the aim of understanding the genetic control of flavonoid accumulation in artichoke, we isolated an artichoke full-length cDNA sequence encoding flavonoid 3′-hydroxylase (F3′H), a major enzyme of the flavonoid hydroxylation pattern. In silico studies confirmed that the deduced amino acid sequence of CcF3′H is highly similar to F3′Hs isolated from other Asteraceae. The Northern blot analysis demonstrated that CcF3′H was highly expressed in leaves and in specific parts of the heads. Its expression differed slightly among artichoke cultivars. The overexpression of CcF3′H in tobacco plants led to the accumulation of flavonoids and to an increase of flower colour intensity, thus identifying CcF3′H as promising candidate for genetic engineering. CcF3′H represents the first structural gene of the flavonoid biosynthesis isolated from C. cardunculus, and its characterization sheds light on the accumulation of flavonoids.     

Leaf flavonoids ofGalium sect.Aparinoides (Rubiaceae)

13 taxa belonging to 4 “species groups” ofGalium L. sect.Aparinoides (Jord.)Gren. produce 15 leaf flavonoids: Apigenin-7-diglucoside, Luteolin-7-monoglucoside and 7-diglucoside, Diosmetin, Diosmetin-7-monoglucoside and 7-diglucoside; Kaempferol-3-rutinoside, Kaempferol-3,7-diglucoside, Quercetin, two Quercetin-3-monoglycosides, Rutin, Quercetin-3-rutinoside-7-glucoside, Quercetin-7-glycoside and an unidentified aglycone. TheG. trifidum, G. obtusum andG. palustre groups (with the exception of theG. tinctorium subspecies andG. elongatum) have similar flavone-flavonole patterns, while theG. antarcticum group produces a specific pattern. Leaf flavonoids of theG. trifidum andG. antarcticum group are inhomogenous, becauseG. tinctorium subsp.tinctorium andG. antarcticum lack flavones. For all taxa (with the exception of those of theG. antarcticum group) intraspecific variation is demonstrated, and 4 populations ofG. trifidum subsp.trifidum, G. tinctorium subsp.tinctorium,G. obtusum subsp.obtusum andG. labradoricum even exhibit intrapopulation variation. The implications of flavonoid data on the systematics and the astonishing intrapopulation and intraspecific variation are discussed.